Package org.gvt.model

Examples of org.gvt.model.IBioPAXEdge


      }
    }

    for (Object o : graph.getEdges())
    {
      IBioPAXEdge edge = (IBioPAXEdge) o;
      if (edge.isHighlighted())
      {
        highlightMap.put(edge.getIDHash(), edge.getHighlightColor());
      }
    }

    // Reset highlight

    HighlightLayer hLayer = (HighlightLayer)
      ((ChsScalableRootEditPart) viewer.getRootEditPart()).getLayer(
        HighlightLayer.HIGHLIGHT_LAYER);

    hLayer.removeAll();
    hLayer.highlighted.clear();

    viewer.deselectAll();

    // Record layout
    graph.recordLayout();

    // Create updated graph
    PathwayHolder p = graph.getPathway();

    // Update pathway components if update needed

    if (withContent != null)
    {
      p.updateContentWith(withContent);
    }

    // Excise pathway

    BioPAXGraph newGraph = main.getRootGraph().excise(p);
    newGraph.setAsRoot();

    // Replace the graph
    viewer.setContents(newGraph);

    // Use same layout
    boolean layedout = newGraph.fetchLayout();

    if (!layedout)
    {
      new CoSELayoutAction(main).run();
    }

    viewer.deselectAll();
    GraphAnimation.run(viewer);

    // Recover highlights

    for (Object o : newGraph.getNodes())
    {
      IBioPAXNode node = (IBioPAXNode) o;
      if (highlightMap.containsKey(node.getIDHash()))
      {
        node.setHighlightColor(highlightMap.get(node.getIDHash()));
        node.setHighlight(true);
      }
    }

    for (Object o : newGraph.getEdges())
    {
      IBioPAXEdge edge = (IBioPAXEdge) o;
      if (highlightMap.containsKey(edge.getIDHash()))
      {
        edge.setHighlightColor(highlightMap.get(edge.getIDHash()));
        edge.setHighlight(true);
      }
    }
  }
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